Contacts of the helix formed by residues 88 - 100 (chain D) in PDB entry 2YEV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D GLY* 4.2 0.2 - - - -
31D TYR* 3.1 40.0 - - + +
83D ILE 5.0 1.3 - - - +
84D GLN* 2.8 46.9 + - - +
87D LEU* 1.3 85.8 - - + +
89D GLY* 1.3 62.6 + - - +
92D ASN* 2.9 32.1 + - - +
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Residues in contact with GLY 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D GLY* 3.6 13.5 - - - +
31D TYR* 3.7 8.1 - - - -
32D THR* 3.1 24.9 + - - -
84D GLN 2.8 10.0 + - - -
85D ALA* 3.4 5.8 - - - -
88D THR* 1.3 80.8 + - - +
90D PHE* 1.3 67.2 + - - +
92D ASN 3.4 4.9 + - - -
93D PHE* 3.4 9.5 + - - +
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Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D THR* 3.8 28.3 - - + -
36D PHE* 3.8 26.9 - + - -
85D ALA* 2.9 23.2 + - + +
86D GLY* 3.7 18.4 - - - +
89D GLY* 1.3 70.8 - - - -
91D GLY* 1.3 52.1 + - - +
93D PHE* 3.2 5.9 + - - +
94D VAL* 2.7 48.9 + - + +
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Residues in contact with GLY 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D GLY 4.3 5.0 + - - -
87D LEU* 3.0 22.4 + - - -
90D PHE* 1.3 78.5 - - - +
92D ASN* 1.3 57.3 + - - +
94D VAL* 5.1 0.7 - - - -
95D VAL* 2.9 49.7 + - - +
96D PRO* 3.6 0.5 - - - +
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Residues in contact with ASN 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D HIS* 2.7 46.2 + - - +
27D ILE* 4.4 8.1 - - - +
28D GLY* 3.8 13.2 - - - +
31D TYR* 3.6 22.8 - - - -
87D LEU 3.8 1.2 + - - -
88D THR* 2.9 34.7 + - - +
89D GLY 3.4 2.2 + - - -
91D GLY* 1.3 74.7 - - - +
93D PHE* 1.3 52.8 + - - +
96D PRO* 3.4 8.8 - - - +
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Residues in contact with PHE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D HIS* 3.3 26.6 + - - -
25D LYS* 3.2 50.5 - - + -
28D GLY* 4.2 3.8 - - - -
29D LEU* 4.0 27.8 - - + -
32D THR* 5.9 0.2 - - - +
89D GLY 3.4 10.0 + - - +
90D PHE* 3.2 9.7 + - - +
92D ASN* 1.3 79.2 - - - +
94D VAL* 1.3 71.8 + - + +
97D LEU* 3.4 27.5 - - + +
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D PHE* 2.7 30.6 + - + +
91D GLY* 5.1 0.4 - - - -
93D PHE* 1.3 89.4 - - + +
95D VAL* 1.3 60.4 + - + +
96D PRO 3.4 1.3 - - - -
97D LEU* 3.0 12.9 + - + +
98D MET* 2.8 60.5 + - + +
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D GLY* 2.9 32.8 + - - +
94D VAL* 1.3 79.2 - - + +
96D PRO* 1.3 65.8 - - + +
98D MET* 3.2 12.2 + - - +
99D LEU* 2.9 43.3 + - + +
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Residues in contact with PRO 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D HIS* 3.4 39.0 - - + +
91D GLY 3.6 1.6 - - - +
92D ASN* 3.4 17.5 - - - +
94D VAL 3.5 3.1 - - - -
95D VAL* 1.3 98.7 - - + +
97D LEU* 1.3 59.1 + - - +
99D LEU* 3.2 8.0 + - + +
100D GLY 3.0 4.2 + - - -
101D ALA* 2.8 45.2 + - + +
102D ARG 5.4 1.6 - - - -
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D HIS* 4.0 17.3 - - + +
25D LYS* 4.7 11.2 - - + +
93D PHE* 3.4 43.1 - - + +
94D VAL* 3.0 12.6 + - + +
96D PRO* 1.3 78.1 - - - +
98D MET* 1.3 58.0 + - + +
100D GLY* 2.9 18.8 + - - -
101D ALA 4.7 8.1 - - - +
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Residues in contact with MET 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D VAL* 2.8 37.6 + - + +
95D VAL* 3.6 15.3 - - - +
97D LEU* 1.3 77.0 - - + +
99D LEU* 1.3 65.9 + - + +
100D GLY 3.1 0.6 + - - -
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D VAL* 2.9 37.9 + - + +
96D PRO* 3.7 7.6 - - + +
97D LEU 3.1 0.2 - - - -
98D MET* 1.3 80.1 - - + +
100D GLY* 1.3 62.3 + - - +
101D ALA* 3.6 9.4 + - + +
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Residues in contact with GLY 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 2.9 17.4 + - - -
98D MET 3.1 1.4 + - - -
99D LEU* 1.3 80.5 - - - +
101D ALA* 1.3 60.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il